PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID KFK34146.1
Organism
Arabis alpina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family C2H2
Protein Properties Length: 769aa    MW: 87855.9 Da    PI: 6.6932
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK34146.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.40.00023651676123
                 EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                 y+C    C++sFs+  +L+ H r+ +
  KFK34146.1 651 YQCDmeGCTMSFSSEKELTLHKRNiC 676
                 99********************9877 PP
2zf-C2H215.83.9e-05676698323
                 ET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                 Cp   Cgk F ++ +L++H+r+H
  KFK34146.1 676 CPekGCGKNFFSHKYLVQHQRVH 698
                 9999*****************99 PP
3zf-C2H213.50.00021734760123
                 EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                 y C   dCg++F+  s++ rH r+  H
  KFK34146.1 734 YICAepDCGQTFRFVSDFSRHKRKtgH 760
                 789999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003557.9651673IPR015880Zinc finger, C2H2-like
SMARTSM003550.012674698IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.173674703IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.8E-7676697IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280676698IPR007087Zinc finger, C2H2
SuperFamilySSF576672.15E-10690732No hitNo description
Gene3DG3DSA:3.30.160.601.8E-9698724IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0018704728IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.866704733IPR007087Zinc finger, C2H2
PROSITE patternPS000280706728IPR007087Zinc finger, C2H2
SuperFamilySSF576674.43E-8722756No hitNo description
Gene3DG3DSA:3.30.160.608.8E-9725757IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.302734765IPR007087Zinc finger, C2H2
SMARTSM003551.4734760IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280736760IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 769 aa     Download sequence    Send to blast
MDQRTSSTSL TKAQKDNDAL GLLASAYGDS SDSEEEDHKG IDVPISEGET RKYDREGACK  60
EEARDGPSSD FNSQRLSRGK EKEVELSHAT TTCSTLSCTS EQNKLTKGDN TSLVGIALPF  120
VLRSDDDSSR LHVFCLEHAA EVEEQLRPIG GIHIMLLCHP EYPRIEAEAK IVAEELGVDH  180
EWNDTEFRNV TQEDEQTIKA ALDNVGTKAG NSDWAVKLGI NLSYSAILSR SPLYSKQMPY  240
NSVIYNLFGR SSPATSSPSK AEVSGKRSSR QRKYVVGKWC GKVWMSHQVH PFLLQQDLEG  300
EESDRSHHLR VALDEDVTGK RLFPGNNSRD ATTMFGRKYS RKRKMRAKAV PRKKLTSFKR  360
EDGVSDDTSE DQSYNQQWRA SDNEEESDFQ IRNTGSGDSS NHMSDHQQLK RNRRQKGVKE  420
FESDDEASDR SLGEEYAVRE DPVSESSMEN SFQLYKQSMD RSALEDSVYG HDDDSIYRHP  480
REISRSKRSK VFKNSVSYDS EENDVYQRSG RKGSRIGGEF DSAEESEEEQ DFRSTGKRQT  540
RSTAKRKVKT EIVKSPRDTK GRALRQCRSR KNSQELDLYM EGPSTRLRVR IQKPSRRSSE  600
IKPKKCGKKR SSIASFSRVA SEEELEEENE EEEEEEEENE EVEEEEECVS YQCDMEGCTM  660
SFSSEKELTL HKRNICPEKG CGKNFFSHKY LVQHQRVHSD DRPLKCPWKG CKMTFKWAWS  720
RTEHVRVHTG ARPYICAEPD CGQTFRFVSD FSRHKRKTGH SVKKTKKGD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-8064876720139Lysine-specific demethylase REF6
6a58_A3e-8064876720139Lysine-specific demethylase REF6
6a59_A3e-8064876720139Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1339344SRKRKM
2341353KRKMRAKAVPRKK
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapKFK34146.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006404260.10.0lysine-specific demethylase REF6
RefseqXP_024013589.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A087GW940.0A0A087GW94_ARAAL; Uncharacterized protein
STRINGA0A087GW940.0(Arabis alpina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  2. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  3. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  4. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  5. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  6. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]